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Crystal structure of xiap-BIR3 domain in complex with smac- mimetic compuond, SMAC005
Analyse Crystal structure of xiap-BIR3 domain in complex with smac- mimetic compuond… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CM7
- Type
- protein
- Length
- 404 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Baculoviral iap repeat-containing protein 4
- EC
- 6.3.2.-
- UniProt
- P98170
- Ligands
- X22, ZN
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Baculoviral iap repeat-containing protein 4 (EC 6.3.2.-) | protein | 102 | 41% helix, 8% strand | P98170 |
| A | Baculoviral iap repeat-containing protein 4 (EC 6.3.2.-) | protein | 101 | 48% helix, 8% strand | P98170 |
| B | Baculoviral iap repeat-containing protein 4 (EC 6.3.2.-) | protein | 101 | 47% helix, 8% strand | P98170 |
| D | Baculoviral iap repeat-containing protein 4 (EC 6.3.2.-) | protein | 100 | 47% helix, 8% strand | P98170 |
Ligands and binding sites
- X22 · (3S,6S,7S,9aS)-6-{[(2S)-2-aminobutanoyl]amino}-N-(diphenylmethyl)-7-(hydroxymethyl)-5-oxooctahydro-1H-pyrrolo[1,2-a]azepine-3-carboxamide · ligand · 6 copies · chains C, B, A, D
- ZN · Zinc ion · metal · 4 copies · chains C, A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1130 | 0.80 | 0.82 | 80 | X22 |
| 2 | 256 | 0.56 | 0.77 | 30 | empty |
| 3 | 54 | 0.29 | 0.75 | 17 | empty |
Interfaces
4 interfaces between chains.
- B–D · 464 Ų buried · 3 hydrogen bonds · protein-protein
- C–A · 338 Ų buried · 2 hydrogen bonds · protein-protein
- C–B · 287 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 227 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3CM7 · Crystal Structure of XIAP-BIR3 domain in complex with Smac-mimetic compuond, Smac005 · the same entry in another collection · chain D against D, TM-score 1.00
- P98170 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase xiap (P98170) · a predicted model of the same protein · chain D against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P98170
- Elsewhere: RCSB PDB 3CM7 · PDBe 3CM7 · UniProt P98170
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